I have saved a sub-site as a template. Then, I created a sub-site based on the template. But it seems that the template will not include the site permissions. So can anyone provide any advice on this?
If you have custom security definitions defined inside your source site, they will not be retained in the template as they cannot be expressed using the declarative language the template uses internally. Your only option really is whether or not to inherit from parent at site creation, as Ransher suggested above.
You'll need to manually recreate the security definitions after site creation, or resort to a code based approach like a WebProvisioned handler.